mgymrek/gangstr_example repository overview

⁠gymreklab-aws-batch

Tutorials and tools for running jobs on AWS batch

⁠Tutorials

• Getting started with AWS Batch (getting_started_batch.md⁠)
• Running a GangSTR job on Batch (gangstr_command_line_example.md⁠)

⁠Resources:

Use these paths for common resources like reference genomes.

• Reference genomes on S3 maintained by Broad: broad-references-readme.html⁠.

  • s3://broad-references/hg19/v0/Homo_sapiens_assembly19.fasta (hg19/GRch37/hs37, no chr)
  • s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta (hg38, chr)

• Other reference genomes:

  • s3://gymreklab/resources/genomes/hg19/hg19.fa (hg19, with chr)